MetaNetX
Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks

SystemsX.ch
The Swiss Initiative in Systems Biology

**This is a beta version of MetaNetX/MNXref, MNXref identifiers may not be final**

Import a model

Select a file and upload it

Options
Input file (see the supported formats below)
Name for it (only alphanumeric and underscore)
Interpret metabolite identifiers	Yes No
Utilize metabolite cross-references	biggM chebi chem envipathM hmdb inchi inchikey keggC keggD keggE keggG lipidmapsM metacycM reactomeM rheaG rheaP sabiorkM seedM slm vmhM

Instructions
What	Comment
Principle	The Import method attempts to upload a user-supplied GEM and map it on the MNXref namespace. An importation report is created that documents the encountered difficulties during the mapping. Various input formats are supported, including all those produced by MetaNetX. Various flavours of the SMBL format are supported, including some idiosyncratic usages of the SBML notes. The use of SBML compliant with the 3.1 specifications is however strongly recommended.
Format	The syntax for text files is given in the model internals documentation. Regarding the SBML file, it is strongly recommended to supply cross references using Identifiers.org-compliant annotations.
Mapping	The following identifiers are recognized and mapped to the MNXref namespace the special identifiers: BIOMASS and BOUNDARY the identifiers describing chemical compounds, i.e. metabolites with the prefix MNXM (e.g. MNXM10) the identifiers describing cellular compartments with the prefix MNXC (e.g. MNXC3); and with the prefix MNXD for the generic compartments the identifiers of the form database:entry are mapped to the MNXref namespace IF possible, e.g. CHEBI:15422. Note that this feature is not supported for SBML model However chemical compounds or cellular compartments not participating in any reaction are automatically removed
General advice	Since, metabolic networks are complex objects combining biochemical, genetic, and genomic information, we recommend new MetaNetX users to practice the following steps Pick a model from the repository (e.g. bigg_iAF1260) Export it as an SBML file, or as a compressed text file (recommended for this exercise) Introduce a small modification in the downloaded model, for example, modify the flux constraints on a single boundary (external) reaction Upload the modified model under a new name Use MetaNetX.org to compare the original model with the modified one
Disclaimer	MetaNetX is not responsible for malformed file or syntax errors and will not offer user support on these issues. We are unfortunately aware that some public genome-scale metabolic networks distributed in SBML format are not 100% compliant with the SBML specifications; or with our editorial choices. As a consequence, their import might be problematic. We recommend checking if a version of such model already exists in the MetaNetX repository.